Data Science in Omics Introduction

An OMICS Course Part 1: Shell, Organizing and Genomics

Creative Commons License

dplyr

Link to Databases


Let’s access an SQL database directly from R using dplyr.

Either use an existing copy of the portal_mammals.sqlite database or download a new copy. You should be able to link to the surveys table in the database using:

library(DBI)
portaldb <- dbConnect(RSQLite::SQLite(), "portal_mammals.sqlite")
surveys <- tbl(portaldb, "surveys")

surveys is actually a connection to the database, which means that the table remains external to the R environment. Also, we won’t need to worry about it printing out huge numbers of rows when we look at it.

  1. Select the year, month, day, and species_id columns in that order.
  2. Create a new data frame with the year, species_id, and weight in kilograms of each individual, with no null weights.
  3. Use the distinct() function to print the species_id for each species in the dataset that has been weighed.
[click here for output] [click here for output]